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Mitchell R. Vollger
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document columns are lists of values in extract
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‎src/fibertools/extracting/extract.md‎

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@@ -36,34 +36,34 @@ All of these files are written in standard bed12 format. The first and last bloc
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### Columns specific to the `--all` output
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| Column | Description |
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| --------------- | -------------------------------------------------------------------------------------------------------------------- |
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| sam_flag | The sam flag of the read alignment |
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| HP | The haplotype tag for the read |
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| RG | The read group tag for the read |
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| fiber_length | The length of the read in bp |
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| fiber_sequence | The sequence of the read |
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| ec | The number of ccs passes for the read (no rounding) |
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| rq | The estimated accuracy of the read |
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| total_AT_bp | The total number of AT bp in the read |
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| total_m6a_bp | The total number of m6a bp in the read |
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| total_nuc_bp | The total number of nucleosome bp in the read |
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| total_msp_bp | The total number of MSP bp in the read |
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| total_5mC_bp | The total number of 5mC bp in the read |
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| nuc_starts | The start positions of the nucleosomes in molecular coordinates |
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| nuc_lengths | The lengths of the nucleosomes in molecular coordinates |
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| ref_nuc_starts | The start positions of the nucleosomes in reference coordinates |
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| ref_nuc_lengths | The lengths of the nucleosomes in reference coordinates |
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| msp_starts | The start positions of the MSPs in molecular coordinates |
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| msp_lengths | The lengths of the MSPs in molecular coordinates |
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| fire | The quality score of the MSP as a FIRE element (if FIRE as been applied). Scores over 230 are FIRE elements [0-255]. |
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| ref_msp_starts | The start positions of the MSPs in reference coordinates |
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| ref_msp_lengths | The lengths of the MSPs in reference coordinates |
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| m6a | The start positions of the m6a in molecular coordinates |
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| ref_m6a | The start positions of the m6a in reference coordinates |
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| m6a_qual | The quality of the m6a positions (ML value) |
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| 5mC | The start positions of the 5mC in molecular coordinates |
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| ref_5mC | The start positions of the 5mC in reference coordinates |
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| 5mC_qual | The quality of the 5mC positions (ML value) |
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| Column | Description |
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| --------------- | ----------------------------------------------------------------------------------------------------------------------------------------------- |
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| sam_flag | The sam flag of the read alignment |
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| HP | The haplotype tag for the read |
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| RG | The read group tag for the read |
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| fiber_length | The length of the read in bp |
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| fiber_sequence | The sequence of the read |
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| ec | The number of ccs passes for the read (no rounding) |
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| rq | The estimated accuracy of the read |
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| total_AT_bp | The total number of AT bp in the read |
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| total_m6a_bp | The total number of m6a bp in the read |
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| total_nuc_bp | The total number of nucleosome bp in the read |
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| total_msp_bp | The total number of MSP bp in the read |
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| total_5mC_bp | The total number of 5mC bp in the read |
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| nuc_starts | The start positions of the nucleosomes in molecular coordinates (comma separated list) |
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| nuc_lengths | The lengths of the nucleosomes in molecular coordinates (comma separated list) |
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| ref_nuc_starts | The start positions of the nucleosomes in reference coordinates (comma separated list) |
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| ref_nuc_lengths | The lengths of the nucleosomes in reference coordinates (comma separated list) |
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| msp_starts | The start positions of the MSPs in molecular coordinates (comma separated list) |
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| msp_lengths | The lengths of the MSPs in molecular coordinates (comma separated list) |
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| fire | The quality score of the MSP as a FIRE element (if FIRE as been applied). Scores over 230 are FIRE elements (comma separated list, range 0-255) |
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| ref_msp_starts | The start positions of the MSPs in reference coordinates (comma separated list) |
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| ref_msp_lengths | The lengths of the MSPs in reference coordinates (comma separated list) |
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| m6a | The start positions of the m6a in molecular coordinates (comma separated list) |
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| ref_m6a | The start positions of the m6a in reference coordinates (comma separated list) |
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| m6a_qual | The quality of the m6a positions (ML value, comma separated list) |
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| 5mC | The start positions of the 5mC in molecular coordinates (comma separated list) |
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| ref_5mC | The start positions of the 5mC in reference coordinates (comma separated list) |
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| 5mC_qual | The quality of the 5mC positions (ML value, comma separated list) |
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Note positions in columns starting with `ref_` maybe contain `-1` (NA) values if the reference sequence has an insertion or deletion relative to the read sequence at that position.

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